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Transfer Learning: Making Retrosynthetic Predictions Based on a Small Chemical Reaction Dataset Scale to a New Level

Artificial Intelligent Aided Drug Discovery Lab, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China
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Molecules 2020, 25(10), 2357; https://doi.org/10.3390/molecules25102357
Received: 5 April 2020 / Revised: 13 May 2020 / Accepted: 14 May 2020 / Published: 19 May 2020
(This article belongs to the Section Computational and Theoretical Chemistry)
Effective computational prediction of complex or novel molecule syntheses can greatly help organic and medicinal chemistry. Retrosynthetic analysis is a method employed by chemists to predict synthetic routes to target compounds. The target compounds are incrementally converted into simpler compounds until the starting compounds are commercially available. However, predictions based on small chemical datasets often result in low accuracy due to an insufficient number of samples. To address this limitation, we introduced transfer learning to retrosynthetic analysis. Transfer learning is a machine learning approach that trains a model on one task and then applies the model to a related but different task; this approach can be used to solve the limitation of few data. The unclassified USPTO-380K large dataset was first applied to models for pretraining so that they gain a basic theoretical knowledge of chemistry, such as the chirality of compounds, reaction types and the SMILES form of chemical structure of compounds. The USPTO-380K and the USPTO-50K (which was also used by Liu et al.) were originally derived from Lowe’s patent mining work. Liu et al. further processed these data and divided the reaction examples into 10 categories, but we did not. Subsequently, the acquired skills were transferred to be used on the classified USPTO-50K small dataset for continuous training and retrosynthetic reaction tests, and the pretrained accuracy data were simultaneously compared with the accuracy of results from models without pretraining. The transfer learning concept was combined with the sequence-to-sequence (seq2seq) or Transformer model for prediction and verification. The seq2seq and Transformer models, both of which are based on an encoder-decoder architecture, were originally constructed for language translation missions. The two algorithms translate SMILES form of structures of reactants to SMILES form of products, also taking into account other relevant chemical information (chirality, reaction types and conditions). The results demonstrated that the accuracy of the retrosynthetic analysis by the seq2seq and Transformer models after pretraining was significantly improved. The top-1 accuracy (which is the accuracy rate of the first prediction matching the actual result) of the Transformer-transfer-learning model increased from 52.4% to 60.7% with greatly improved prediction power. The model’s top-20 prediction accuracy (which is the accuracy rate of the top 20 categories containing actual results) was 88.9%, which represents fairly good prediction in retrosynthetic analysis. In summary, this study proves that transferring learning between models working with different chemical datasets is feasible. The introduction of transfer learning to a model significantly improved prediction accuracy and, especially, assisted in small dataset based reaction prediction and retrosynthetic analysis. View Full-Text
Keywords: retrosynthesis; SMILES structure; reactants; products; transfer leaning; artificial intelligence; transformer; seq2seq retrosynthesis; SMILES structure; reactants; products; transfer leaning; artificial intelligence; transformer; seq2seq
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MDPI and ACS Style

Bai, R.; Zhang, C.; Wang, L.; Yao, C.; Ge, J.; Duan, H. Transfer Learning: Making Retrosynthetic Predictions Based on a Small Chemical Reaction Dataset Scale to a New Level. Molecules 2020, 25, 2357.

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